Rapid reconstruction of multidrug-resistant bacterial genomes using CycloneSEQ nanopore sequencing.

Authors

Kai Peng, Zeyu Tong, Changan Li, Zhichao Li, Xin Lu, Cemil Kurekci, Mashkoor Mohsin, Zhiqiang Wang, Yong-Xin Liu, Ruichao Li

Published in

iMetaOmics. Volume 3. Issue 1. Pages e70060. Epub Oct 26, 2025.

Abstract

Multidrug-resistant (MDR) bacteria commonly harbor highly complex genomes enriched with mobile elements and resistance islands, which are challenging to resolve using short-read sequencing. Here, we evaluated CycloneSEQ, a newly developed Chinese nanopore sequencing platform, for MDR genome reconstruction. Long-read-only assemblies generated near-complete genomes, while hybrid assemblies achieved accuracy exceeding 99.99%. CycloneSEQ effectively resolved complex structures, including tandem repeats within ARG-bearing regions. Notably, updated sequencing chemistry improved single-read accuracy to 96.2% and yielded assembled genomes with 99.98% accuracy. These results demonstrate that CycloneSEQ enables the generation of complete and highly accurate bacterial genomes, highlighting its potential for antimicrobial resistance research and clinical surveillance.

PMID:
42891306
Bibliographic data and abstract were imported from PubMed on 18 Oct 2026.

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